ggbio (version 1.20.0)

plotGrandLinear: Manhattan for GWAS

Description

A Manhattan plot is special scatter plot used to visualize data with a large number of data points, with a distribute of some higher-magnitude values. For example, in the GWAS(genome-wide association studies). Here we mainly focus on GWAS Manhattan plots. X-axis is genomic coordinates and Y-axis is negative logarithm of the associated P-value for each single nucleotide polymorphism. So higher the value, more stronger the association they are.

Usage

plotGrandLinear(obj, ..., facets, space.skip = 0.01, geom = NULL, cutoff = NULL, cutoff.color = "red", cutoff.size = 1, legend = FALSE, xlim, ylim, xlab, ylab, main, highlight.gr = NULL, highlight.name = NULL, highlight.col = "red", highlight.label = TRUE, highlight.label.size = 5, highlight.label.offset = 0.05, highlight.label.col = "black", spaceline = FALSE)

Arguments

obj

GRanges object which contains extra p value, before users pass this object, they need to make sure the pvalue has been changed to -log10(p).

...

extra arguments passed. such as color, size, alpha.

facets

facets formula, such as group ~ .

space.skip

numeric value for skip ratio, between chromosome spaces.default is 0.01.

geom

geometric object, defualt is "point".

cutoff

A numeric vector which used as cutoff for Manhattan plot.

cutoff.color

A character specifying the color used for cutoff. Default is "red".

cutoff.size

A numeric value which used as cutoff line size.

legend

A logical value indicate whether to show legend or not. Default is FALSE which disabled the legend.

xlim

limits for x scale.

ylim

limits for y scale.

xlab

Label for xscale.

ylab

Label for yscale.

main

title.

highlight.gr

a GRanges object, this wil highlight overlapped region with provided intervals.

highlight.name

if NULL, using rownames of GRanges object provided by argument highlight.gr, otherwise use character to indicate column used as labeled names.

highlight.col

highlight colors.

highlight.label

logical value, label the highlighted region of not.

highlight.label.size

highlight label size.

highlight.label.offset

highlight label offset.

highlight.label.col

highlight label color.

spaceline

show line between chromosomes.

Value

Return a ggplot object.

Details

Please use seqlengths of the object and space.skip arguments to control the layout of the coordiant genome transformation.

aes(y = ...) is requried.

aes(color = ) is used to mapping to data variables, if just pass "color" without aes(), then will recycle the color to represent each chromosomes.please see the example below.

Examples

##  load
library(ggbio)
data(hg19IdeogramCyto, package = "biovizBase")
data(hg19Ideogram, package = "biovizBase")
library(GenomicRanges)

##  simul_gr
library(biovizBase)
gr <- GRanges(rep(c("chr1", "chr2"), each = 5),
              IRanges(start = rep(seq(1, 100, length = 5), times = 2),
                      width = 50))
autoplot(gr)

##  coord:genome
autoplot(gr, coord = "genome")
gr.t <- transformToGenome(gr)
head(gr.t)

##  is
is_coord_genome(gr.t)
metadata(gr.t)$coord


##  simul_snp
chrs <- as.character(levels(seqnames(hg19IdeogramCyto)))
seqlths <- seqlengths(hg19Ideogram)[chrs]
set.seed(1)
nchr <- length(chrs)
nsnps <- 100
gr.snp <- GRanges(rep(chrs,each=nsnps),
                  IRanges(start =
                          do.call(c, lapply(chrs, function(chr){
                            N <- seqlths[chr]
                            runif(nsnps,1,N)
                          })), width = 1),
                  SNP=sapply(1:(nchr*nsnps), function(x) paste("rs",x,sep='')),
                  pvalue =  -log10(runif(nchr*nsnps)),
                  group = sample(c("Normal", "Tumor"), size = nchr*nsnps,
                    replace = TRUE)
                  )

##  shorter
seqlengths(gr.snp)
nms <- seqnames(seqinfo(gr.snp))
nms.new <- gsub("chr", "", nms)
names(nms.new) <- nms
gr.snp <- renameSeqlevels(gr.snp, nms.new)
seqlengths(gr.snp)



##  unorder
autoplot(gr.snp, coord = "genome", geom = "point", aes(y = pvalue), space.skip = 0.01)

##  sort
gr.snp <- keepSeqlevels(gr.snp, c(1:22, "X", "Y"))
autoplot(gr.snp, coord = "genome", geom = "point", aes(y = pvalue), space.skip = 0.01)

##  with_seql
names(seqlths) <- gsub("chr", "", names(seqlths))
seqlengths(gr.snp) <- seqlths[names(seqlengths(gr.snp))]
autoplot(gr.snp, coord = "genome", geom = "point", aes(y = pvalue), space.skip = 0.01)

##  line
autoplot(gr.snp, coord = "genome", geom = "line", aes(y = pvalue, group = seqnames,
                                     color = seqnames))



##  plotGrandLinear
plotGrandLinear(gr.snp, aes(y = pvalue))

##  morecolor
plotGrandLinear(gr.snp, aes(y = pvalue, color = seqnames))
plotGrandLinear(gr.snp, aes(y = pvalue), color = c("green", "deepskyblue"))
plotGrandLinear(gr.snp, aes(y = pvalue), color = c("green", "deepskyblue", "red"))
plotGrandLinear(gr.snp, aes(y = pvalue), color = "red")

##  cutoff
plotGrandLinear(gr.snp, aes(y = pvalue), cutoff = 3, cutoff.color = "blue", cutoff.size = 4)

##  cutoff-low
plotGrandLinear(gr.snp, aes(y = pvalue)) + geom_hline(yintercept = 3, color = "blue", size = 4)

##  longer
## let's make a long name
nms <- seqnames(seqinfo(gr.snp))
nms.new <- paste("chr00000", nms, sep = "")
names(nms.new) <- nms
gr.snp <- renameSeqlevels(gr.snp, nms.new)
seqlengths(gr.snp)

##  rotate
plotGrandLinear(gr.snp, aes(y = pvalue)) + theme(axis.text.x=element_text(angle=-90, hjust=0))

##  sessionInfo
sessionInfo()